Limits...
Gene conversion in the rice genome.

Xu S, Clark T, Zheng H, Vang S, Li R, Wong GK, Wang J, Zheng X - BMC Genomics (2008)

Bottom Line: We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05).The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners.The number of conversions associated with segmentation is less than ten percent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China. shuqing.xu@env.ethz.ch

ABSTRACT

Background: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion.

Results: To characterize gene conversion in rice, we have defined 626 multigene families in which 377 gene conversions were detected using the GENECONV program. Over 60% of the conversions we detected were between chromosomes. We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05). The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners. Ka/Ks analysis indicates that gene conversion is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less than ten percent. Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes. Functional annotations suggest that at least 14 multigene families related to disease or bacteria resistance were involved in conversion events.

Conclusion: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes.

Show MeSH
Gene conversion distribution on the twelve rice chromosomes. The two genes in each gene pair identified in a conversion are connected with a line. The line thickness indicates the frequency of the gene conversion between the corresponding chromosomes. The highest inter-chromosomal conversion frequencies were detected between chromosomes 1 and 5, 2 and 6, and 3 and 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2277409&req=5

Figure 2: Gene conversion distribution on the twelve rice chromosomes. The two genes in each gene pair identified in a conversion are connected with a line. The line thickness indicates the frequency of the gene conversion between the corresponding chromosomes. The highest inter-chromosomal conversion frequencies were detected between chromosomes 1 and 5, 2 and 6, and 3 and 5.

Mentions: The 229 inter-chromosomal conversion events are distributed non-uniformly among the twelve chromosomes of the rice genome. The conversion events are significantly more frequent between chromosomes 1 and 5, 2 and 6, and 3 and 5 than the average (Z-test, P < 0.05). The conversion distributions are shown in Figure 2 for each chromosome.


Gene conversion in the rice genome.

Xu S, Clark T, Zheng H, Vang S, Li R, Wong GK, Wang J, Zheng X - BMC Genomics (2008)

Gene conversion distribution on the twelve rice chromosomes. The two genes in each gene pair identified in a conversion are connected with a line. The line thickness indicates the frequency of the gene conversion between the corresponding chromosomes. The highest inter-chromosomal conversion frequencies were detected between chromosomes 1 and 5, 2 and 6, and 3 and 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277409&req=5

Figure 2: Gene conversion distribution on the twelve rice chromosomes. The two genes in each gene pair identified in a conversion are connected with a line. The line thickness indicates the frequency of the gene conversion between the corresponding chromosomes. The highest inter-chromosomal conversion frequencies were detected between chromosomes 1 and 5, 2 and 6, and 3 and 5.
Mentions: The 229 inter-chromosomal conversion events are distributed non-uniformly among the twelve chromosomes of the rice genome. The conversion events are significantly more frequent between chromosomes 1 and 5, 2 and 6, and 3 and 5 than the average (Z-test, P < 0.05). The conversion distributions are shown in Figure 2 for each chromosome.

Bottom Line: We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05).The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners.The number of conversions associated with segmentation is less than ten percent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China. shuqing.xu@env.ethz.ch

ABSTRACT

Background: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion.

Results: To characterize gene conversion in rice, we have defined 626 multigene families in which 377 gene conversions were detected using the GENECONV program. Over 60% of the conversions we detected were between chromosomes. We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05). The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners. Ka/Ks analysis indicates that gene conversion is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less than ten percent. Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes. Functional annotations suggest that at least 14 multigene families related to disease or bacteria resistance were involved in conversion events.

Conclusion: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes.

Show MeSH